DUUUUUUUUUUUDE.
Spot on. I really wish you were designing Crysis 3.
Per weapon balance... fixing the scar+laser bug is a no brainer. I'm pretty sure there will be a whole troop down to murder.
I think the balance of the other weapons is pretty decent right now, with the exception of the FY. The L-tag is an awesome fun weapon, but spammers have ruined it for everyone. Also, more options for unlocking weapons would be nice. Grinding is stupid. Especially after five reboots. -__-
I personally would like to see some more RPG features. NS customization, as you mentioned. But modules should also interact and have bonuses/downfalls (like you mentioned for SE/ME, or Armor enhance III improving reload time with Weapon pro). And I definitely agree on having multiple combos on modules. I love your ideas there.
Also, more custom class slots. Maybe have it so that you unlock them with hours of gameplay. Reward the players who give their all.
Rebooting. It's cute. Like CoD. But seriously, loosing all your perks, weapon unlocks (which you have to grind for), and weapon stats (ie, SCAR Kills) is just stupid. ESPECIALLY if you got autorebooted like... oh, i dunno. Most of the community?
I know i'm ranting, but lol... it would be fun.